Multiple sequence alignment - TraesCS3B01G390900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G390900 chr3B 100.000 3884 0 0 1 3884 616181362 616185245 0.000000e+00 7173
1 TraesCS3B01G390900 chr3D 93.620 2743 97 30 706 3417 463083172 463080477 0.000000e+00 4024
2 TraesCS3B01G390900 chr3D 89.094 651 29 10 49 660 463084015 463083368 0.000000e+00 771
3 TraesCS3B01G390900 chr3D 88.688 221 17 4 3664 3884 463079927 463079715 2.980000e-66 263
4 TraesCS3B01G390900 chr3D 89.080 174 5 5 3457 3629 463080472 463080312 1.830000e-48 204
5 TraesCS3B01G390900 chr3D 94.309 123 6 1 1 122 463084117 463083995 1.840000e-43 187
6 TraesCS3B01G390900 chr3A 91.166 2728 127 56 831 3503 606424786 606427454 0.000000e+00 3598
7 TraesCS3B01G390900 chr3A 84.715 772 70 20 48 802 606423975 606424715 0.000000e+00 728
8 TraesCS3B01G390900 chr4B 78.718 390 77 6 1539 1924 438226858 438226471 4.980000e-64 255
9 TraesCS3B01G390900 chr4A 78.462 390 78 6 1539 1924 110379664 110380051 2.320000e-62 250
10 TraesCS3B01G390900 chr4D 77.949 390 80 6 1539 1924 354146084 354145697 5.020000e-59 239


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G390900 chr3B 616181362 616185245 3883 False 7173.0 7173 100.0000 1 3884 1 chr3B.!!$F1 3883
1 TraesCS3B01G390900 chr3D 463079715 463084117 4402 True 1089.8 4024 90.9582 1 3884 5 chr3D.!!$R1 3883
2 TraesCS3B01G390900 chr3A 606423975 606427454 3479 False 2163.0 3598 87.9405 48 3503 2 chr3A.!!$F1 3455

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
294 372 0.178301 TCACCACGGCACAGTAACAA 59.822 50.0 0.0 0.0 0.00 2.83 F
1681 2011 0.454957 CGCATTTCCCTTTCAGCGTG 60.455 55.0 0.0 0.0 40.25 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2086 0.324943 AACTCACCACCTCAATCCCG 59.675 55.0 0.0 0.0 0.0 5.14 R
3655 4026 0.319728 CTCCTGTCTGTGTCCTGGTG 59.680 60.0 0.0 0.0 0.0 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 0.532115 CCAACTAGGGTGGCATTTGC 59.468 55.000 2.07 0.00 41.14 3.68
121 177 1.665442 GTGGCATTTTGCGAACCCT 59.335 52.632 0.00 0.00 46.21 4.34
156 212 7.849515 CAGTTTGTTTAACTACGAAGAGGTTTC 59.150 37.037 0.00 0.00 45.29 2.78
180 237 1.021202 CAAAACTGCCACCGTCAGAA 58.979 50.000 0.00 0.00 35.61 3.02
210 267 1.092348 GTTTGCCACGATTAGGTCCC 58.908 55.000 0.00 0.00 0.00 4.46
215 272 1.191535 CCACGATTAGGTCCCTGACA 58.808 55.000 0.00 0.00 33.68 3.58
227 284 0.580104 CCCTGACAAACGTTCGTCAC 59.420 55.000 17.79 0.00 37.23 3.67
247 304 8.402472 TCGTCACACAACATTCTAAAGAAAAAT 58.598 29.630 0.00 0.00 37.61 1.82
294 372 0.178301 TCACCACGGCACAGTAACAA 59.822 50.000 0.00 0.00 0.00 2.83
317 395 5.880054 ACTAGAAATGCAACAAATACGCT 57.120 34.783 0.00 0.00 0.00 5.07
320 398 4.647964 AGAAATGCAACAAATACGCTACG 58.352 39.130 0.00 0.00 0.00 3.51
604 718 4.082523 CGCTTCCGAGCCCCAGAA 62.083 66.667 0.00 0.00 46.42 3.02
606 720 2.660064 GCTTCCGAGCCCCAGAAGA 61.660 63.158 3.28 0.00 43.29 2.87
622 736 1.467342 GAAGACAATAAAAGCGGCCGT 59.533 47.619 28.70 11.01 0.00 5.68
732 997 1.467374 CCACCCGAGCTAAAAATTGCG 60.467 52.381 0.00 0.00 0.00 4.85
821 1095 1.265454 CCTAGCAAGTTCTCCGGGGT 61.265 60.000 0.00 0.00 0.00 4.95
897 1204 1.153568 CATGGAGTGGTCGCACGAT 60.154 57.895 0.00 0.00 0.00 3.73
1543 1873 1.079127 CCTCCGGCTCGACATGTTT 60.079 57.895 0.00 0.00 0.00 2.83
1681 2011 0.454957 CGCATTTCCCTTTCAGCGTG 60.455 55.000 0.00 0.00 40.25 5.34
1738 2068 3.528370 CACTACCGGGGCCTCTCG 61.528 72.222 6.32 3.72 0.00 4.04
1756 2086 2.672996 AACCCGCAGTGCATCCAC 60.673 61.111 16.83 0.00 42.39 4.02
1762 2092 1.750399 GCAGTGCATCCACGGGATT 60.750 57.895 11.09 0.00 46.62 3.01
1798 2128 0.460109 CGAATCTCGTGGGCATCACA 60.460 55.000 9.55 0.00 46.36 3.58
1876 2206 1.078143 ACAGGAGGCCAGCGATTTC 60.078 57.895 5.01 0.00 0.00 2.17
1933 2263 1.376466 GGAGAGGCCACACACACAT 59.624 57.895 5.01 0.00 36.34 3.21
1934 2264 0.674895 GGAGAGGCCACACACACATC 60.675 60.000 5.01 0.00 36.34 3.06
1972 2302 7.067372 AGCAATACTAATAATGTTCAGCAGCAA 59.933 33.333 0.00 0.00 0.00 3.91
2017 2347 4.497006 GGATCAGGCTTGAATTTGTCATCG 60.497 45.833 1.33 0.00 36.78 3.84
2044 2374 2.166907 ATCATTCAGGAGAGGACGGT 57.833 50.000 0.00 0.00 0.00 4.83
2137 2467 1.073897 GCCTCTGAACCCTTGCACT 59.926 57.895 0.00 0.00 0.00 4.40
2170 2500 3.894920 ACAAGATATCGAGATGCAGTCG 58.105 45.455 13.69 13.69 38.84 4.18
2305 2635 4.391830 GTCAGCTTACCATTTGTCGATCAA 59.608 41.667 0.00 0.00 0.00 2.57
2317 2647 4.610605 TGTCGATCAACAGAGGGTAAAA 57.389 40.909 0.00 0.00 0.00 1.52
2338 2668 4.713792 AGTTTCATGGAAGAACACTCCT 57.286 40.909 0.00 0.00 0.00 3.69
2368 2698 7.377766 TGGCATAGTTAAAATCTTCTGTGTC 57.622 36.000 0.00 0.00 0.00 3.67
2497 2827 1.119574 CCACCCGTATCCCCGAAGAT 61.120 60.000 0.00 0.00 0.00 2.40
2587 2917 2.427506 GAGCCGGAAGAACATGAAGTT 58.572 47.619 5.05 0.00 44.93 2.66
2663 2997 6.240549 AGGTAATGGAAGGTCTATCTTGTG 57.759 41.667 0.00 0.00 0.00 3.33
2741 3079 0.667993 TTGCTGTTGCTTACTGTGCC 59.332 50.000 0.00 0.00 40.48 5.01
2742 3080 0.179020 TGCTGTTGCTTACTGTGCCT 60.179 50.000 0.00 0.00 40.48 4.75
2928 3276 6.095377 GGTTACTGCTCAATTTTTGGATCTG 58.905 40.000 0.00 0.00 0.00 2.90
2936 3284 8.853126 TGCTCAATTTTTGGATCTGGATTATAG 58.147 33.333 0.00 0.00 0.00 1.31
2937 3285 8.854117 GCTCAATTTTTGGATCTGGATTATAGT 58.146 33.333 0.00 0.00 0.00 2.12
2993 3344 6.586344 TCCCAAATTTACAATGTTCTTTGCA 58.414 32.000 0.00 0.00 0.00 4.08
3001 3352 9.683069 ATTTACAATGTTCTTTGCAGTTAAGAG 57.317 29.630 0.00 0.00 33.49 2.85
3090 3441 0.464036 TGTCCCGATCAGCATACACC 59.536 55.000 0.00 0.00 0.00 4.16
3099 3450 4.564041 GATCAGCATACACCATACAGGAG 58.436 47.826 0.00 0.00 41.22 3.69
3114 3465 1.068748 CAGGAGTTGTTGATGCAGCAC 60.069 52.381 2.94 0.25 0.00 4.40
3115 3466 1.202855 AGGAGTTGTTGATGCAGCACT 60.203 47.619 2.94 0.00 0.00 4.40
3116 3467 1.068748 GGAGTTGTTGATGCAGCACTG 60.069 52.381 2.94 0.00 0.00 3.66
3216 3571 2.354510 TCTTGCAACTGGAGTTTTCACG 59.645 45.455 0.00 0.00 35.83 4.35
3256 3611 5.455872 TCCTCCATCTTACTTACTACTGGG 58.544 45.833 0.00 0.00 0.00 4.45
3259 3614 4.960469 TCCATCTTACTTACTACTGGGTGG 59.040 45.833 0.00 0.00 0.00 4.61
3266 3621 3.858247 CTTACTACTGGGTGGTAAGCAC 58.142 50.000 16.60 0.00 45.36 4.40
3267 3622 0.606604 ACTACTGGGTGGTAAGCACG 59.393 55.000 0.00 0.00 0.00 5.34
3268 3623 0.892755 CTACTGGGTGGTAAGCACGA 59.107 55.000 0.00 0.00 0.00 4.35
3269 3624 1.480954 CTACTGGGTGGTAAGCACGAT 59.519 52.381 0.00 0.00 0.00 3.73
3270 3625 0.690762 ACTGGGTGGTAAGCACGATT 59.309 50.000 0.00 0.00 0.00 3.34
3273 3628 0.808755 GGGTGGTAAGCACGATTTGG 59.191 55.000 0.00 0.00 0.00 3.28
3304 3659 1.067295 TCCTGGAAGCTGGTGAACAT 58.933 50.000 0.00 0.00 0.00 2.71
3306 3661 1.004044 CCTGGAAGCTGGTGAACATCT 59.996 52.381 0.00 0.00 0.00 2.90
3307 3662 2.237143 CCTGGAAGCTGGTGAACATCTA 59.763 50.000 0.00 0.00 0.00 1.98
3308 3663 3.529533 CTGGAAGCTGGTGAACATCTAG 58.470 50.000 0.00 0.00 0.00 2.43
3309 3664 2.906389 TGGAAGCTGGTGAACATCTAGT 59.094 45.455 0.00 0.00 0.00 2.57
3310 3665 4.093743 TGGAAGCTGGTGAACATCTAGTA 58.906 43.478 0.00 0.00 0.00 1.82
3417 3772 3.120060 GCTCAACATAAGCTGTCTTGTGG 60.120 47.826 11.10 0.00 43.21 4.17
3424 3779 3.498774 AAGCTGTCTTGTGGTGATCTT 57.501 42.857 0.00 0.00 0.00 2.40
3426 3781 2.636893 AGCTGTCTTGTGGTGATCTTCT 59.363 45.455 0.00 0.00 0.00 2.85
3427 3782 2.999355 GCTGTCTTGTGGTGATCTTCTC 59.001 50.000 0.00 0.00 0.00 2.87
3428 3783 3.594134 CTGTCTTGTGGTGATCTTCTCC 58.406 50.000 0.00 0.00 0.00 3.71
3430 3785 3.584406 TGTCTTGTGGTGATCTTCTCCAT 59.416 43.478 2.01 0.00 41.43 3.41
3432 3787 4.081198 GTCTTGTGGTGATCTTCTCCATCT 60.081 45.833 2.01 0.00 41.43 2.90
3433 3788 4.533707 TCTTGTGGTGATCTTCTCCATCTT 59.466 41.667 2.01 0.00 41.43 2.40
3434 3789 5.721480 TCTTGTGGTGATCTTCTCCATCTTA 59.279 40.000 2.01 0.00 41.43 2.10
3435 3790 5.344743 TGTGGTGATCTTCTCCATCTTAC 57.655 43.478 2.01 0.00 41.43 2.34
3436 3791 5.026121 TGTGGTGATCTTCTCCATCTTACT 58.974 41.667 2.01 0.00 41.43 2.24
3437 3792 5.485353 TGTGGTGATCTTCTCCATCTTACTT 59.515 40.000 2.01 0.00 41.43 2.24
3438 3793 6.667848 TGTGGTGATCTTCTCCATCTTACTTA 59.332 38.462 2.01 0.00 41.43 2.24
3439 3794 7.345653 TGTGGTGATCTTCTCCATCTTACTTAT 59.654 37.037 2.01 0.00 41.43 1.73
3440 3795 8.861086 GTGGTGATCTTCTCCATCTTACTTATA 58.139 37.037 2.01 0.00 41.43 0.98
3441 3796 8.861086 TGGTGATCTTCTCCATCTTACTTATAC 58.139 37.037 0.00 0.00 35.34 1.47
3442 3797 9.084533 GGTGATCTTCTCCATCTTACTTATACT 57.915 37.037 0.00 0.00 30.74 2.12
3447 3802 9.796180 TCTTCTCCATCTTACTTATACTACTCC 57.204 37.037 0.00 0.00 0.00 3.85
3448 3803 9.575868 CTTCTCCATCTTACTTATACTACTCCA 57.424 37.037 0.00 0.00 0.00 3.86
3449 3804 9.931698 TTCTCCATCTTACTTATACTACTCCAA 57.068 33.333 0.00 0.00 0.00 3.53
3496 3867 5.440234 TTGTTGATCTCTATCTACTCCGC 57.560 43.478 0.00 0.00 38.30 5.54
3542 3913 4.037208 AGTGAAGTTTCAAGGCAACAGATG 59.963 41.667 0.00 0.00 39.21 2.90
3547 3918 6.655078 AGTTTCAAGGCAACAGATGTTATT 57.345 33.333 0.00 0.00 36.32 1.40
3548 3919 7.759489 AGTTTCAAGGCAACAGATGTTATTA 57.241 32.000 0.00 0.00 36.32 0.98
3549 3920 8.177119 AGTTTCAAGGCAACAGATGTTATTAA 57.823 30.769 0.00 0.00 36.32 1.40
3550 3921 8.082242 AGTTTCAAGGCAACAGATGTTATTAAC 58.918 33.333 0.00 0.00 36.32 2.01
3551 3922 7.517614 TTCAAGGCAACAGATGTTATTAACA 57.482 32.000 11.47 11.47 43.14 2.41
3589 3960 2.157668 CCTAACAACTGCTGCTTGTACG 59.842 50.000 7.57 3.08 31.43 3.67
3603 3974 2.092882 GTACGTGCCTGTTCCGCTC 61.093 63.158 0.00 0.00 0.00 5.03
3617 3988 2.231529 TCCGCTCTAGGTTCAGATAGC 58.768 52.381 0.00 0.00 0.00 2.97
3619 3990 2.030363 CCGCTCTAGGTTCAGATAGCTG 60.030 54.545 0.24 0.24 43.67 4.24
3620 3991 2.606795 CGCTCTAGGTTCAGATAGCTGC 60.607 54.545 2.24 0.00 42.01 5.25
3621 3992 2.363680 GCTCTAGGTTCAGATAGCTGCA 59.636 50.000 2.24 0.00 42.01 4.41
3622 3993 3.552684 GCTCTAGGTTCAGATAGCTGCAG 60.553 52.174 10.11 10.11 42.01 4.41
3629 4000 2.203266 GATAGCTGCAGCCCCCAC 60.203 66.667 34.39 17.53 43.38 4.61
3697 4433 3.741476 CTGCTCAGCAAACGGGGC 61.741 66.667 0.00 0.00 38.41 5.80
3707 4443 0.246360 CAAACGGGGCCCAAGAATTC 59.754 55.000 26.86 2.37 0.00 2.17
3724 4460 1.640428 TTCGCTACAATCTGCTTCGG 58.360 50.000 0.00 0.00 0.00 4.30
3730 4466 3.430374 GCTACAATCTGCTTCGGAACCTA 60.430 47.826 0.00 0.00 0.00 3.08
3731 4467 3.252974 ACAATCTGCTTCGGAACCTAG 57.747 47.619 0.00 0.00 0.00 3.02
3732 4468 1.936547 CAATCTGCTTCGGAACCTAGC 59.063 52.381 7.53 7.53 35.50 3.42
3733 4469 1.490574 ATCTGCTTCGGAACCTAGCT 58.509 50.000 13.12 0.00 35.93 3.32
3734 4470 0.532573 TCTGCTTCGGAACCTAGCTG 59.467 55.000 0.00 12.55 35.93 4.24
3736 4472 1.079127 GCTTCGGAACCTAGCTGCA 60.079 57.895 1.02 0.00 32.26 4.41
3737 4473 1.362406 GCTTCGGAACCTAGCTGCAC 61.362 60.000 1.02 0.00 32.26 4.57
3738 4474 0.741221 CTTCGGAACCTAGCTGCACC 60.741 60.000 1.02 0.00 0.00 5.01
3739 4475 1.192146 TTCGGAACCTAGCTGCACCT 61.192 55.000 1.02 0.00 0.00 4.00
3740 4476 1.153549 CGGAACCTAGCTGCACCTC 60.154 63.158 1.02 0.00 0.00 3.85
3759 4495 1.688735 TCCTGGACCTGCTCGATAATG 59.311 52.381 0.00 0.00 0.00 1.90
3761 4497 1.688735 CTGGACCTGCTCGATAATGGA 59.311 52.381 0.00 0.00 0.00 3.41
3762 4498 2.103094 CTGGACCTGCTCGATAATGGAA 59.897 50.000 0.00 0.00 0.00 3.53
3763 4499 2.103094 TGGACCTGCTCGATAATGGAAG 59.897 50.000 0.00 0.00 0.00 3.46
3764 4500 2.139118 GACCTGCTCGATAATGGAAGC 58.861 52.381 0.00 0.00 0.00 3.86
3765 4501 1.486310 ACCTGCTCGATAATGGAAGCA 59.514 47.619 0.00 0.00 0.00 3.91
3772 4508 3.591023 TCGATAATGGAAGCACACGAAA 58.409 40.909 0.00 0.00 0.00 3.46
3803 4539 1.088340 CATTCTGCTGACGCCTCCTG 61.088 60.000 0.00 0.00 34.43 3.86
3827 4563 3.334054 GGGCCTGAACCTGCTCCT 61.334 66.667 0.84 0.00 0.00 3.69
3828 4564 2.270527 GGCCTGAACCTGCTCCTC 59.729 66.667 0.00 0.00 0.00 3.71
3838 4574 3.719883 CTGCTCCTCCTCTGCGCTG 62.720 68.421 9.73 8.88 0.00 5.18
3841 4577 3.429080 CTCCTCCTCTGCGCTGCTC 62.429 68.421 9.73 0.00 0.00 4.26
3845 4581 2.018727 CTCCTCTGCGCTGCTCAGAT 62.019 60.000 21.21 0.00 39.56 2.90
3848 4584 1.481019 CTCTGCGCTGCTCAGATTCG 61.481 60.000 21.21 7.74 39.56 3.34
3860 4596 3.070018 CTCAGATTCGAAGCCACAACTT 58.930 45.455 10.29 0.00 0.00 2.66
3870 4606 2.576615 AGCCACAACTTCCTGTTTCTC 58.423 47.619 0.00 0.00 36.63 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.373570 GAACTTTCGCCAGCTAGCAT 58.626 50.000 18.83 0.00 0.00 3.79
20 21 1.014044 CGAACTTTCGCCAGCTAGCA 61.014 55.000 18.83 0.00 44.26 3.49
59 60 4.094887 CACTAAAATGTCATCAGGGGTTCG 59.905 45.833 0.00 0.00 0.00 3.95
121 177 3.371591 AGTTAAACAAACTGCGACGTCAA 59.628 39.130 17.16 1.73 46.90 3.18
146 202 2.357952 AGTTTTGTGCCGAAACCTCTTC 59.642 45.455 12.01 0.00 38.20 2.87
180 237 2.665185 GGCAAACGCCTCAGACGT 60.665 61.111 0.00 0.00 46.85 4.34
215 272 3.372822 AGAATGTTGTGTGACGAACGTTT 59.627 39.130 0.46 0.00 32.64 3.60
247 304 2.305927 CCTTTTGAGGGCTTGTCCTAGA 59.694 50.000 0.00 0.00 37.25 2.43
251 308 1.889170 CTTCCTTTTGAGGGCTTGTCC 59.111 52.381 0.00 0.00 0.00 4.02
294 372 6.254281 AGCGTATTTGTTGCATTTCTAGTT 57.746 33.333 0.00 0.00 0.00 2.24
317 395 1.406887 GCTCATGGCCTTTCTTCCGTA 60.407 52.381 3.32 0.00 34.27 4.02
520 634 3.770040 TCATCTCCACGCCCACGG 61.770 66.667 0.00 0.00 46.04 4.94
604 718 1.084289 GACGGCCGCTTTTATTGTCT 58.916 50.000 28.58 0.00 0.00 3.41
606 720 1.310216 GGGACGGCCGCTTTTATTGT 61.310 55.000 28.58 0.57 33.83 2.71
634 748 2.290387 GGTGGAAGAAAGGGAAGAGGTC 60.290 54.545 0.00 0.00 0.00 3.85
719 984 4.237724 GGAAAGCTTCGCAATTTTTAGCT 58.762 39.130 0.00 0.00 43.58 3.32
732 997 1.740025 CACCTCCATTCGGAAAGCTTC 59.260 52.381 0.00 0.00 42.21 3.86
821 1095 4.022416 CACAAATCTGAACCAAATCCGGAA 60.022 41.667 9.01 0.00 0.00 4.30
1333 1660 4.436998 ACGGCCTCGGCTTCGAAG 62.437 66.667 21.02 21.02 42.80 3.79
1543 1873 1.668793 CATGTCGTGCTGCACCAGA 60.669 57.895 25.61 13.47 32.44 3.86
1612 1942 2.692817 GCTCCTCAGCTGCATCTTC 58.307 57.895 9.47 0.00 43.09 2.87
1738 2068 2.359850 TGGATGCACTGCGGGTTC 60.360 61.111 0.00 0.00 0.00 3.62
1756 2086 0.324943 AACTCACCACCTCAATCCCG 59.675 55.000 0.00 0.00 0.00 5.14
1762 2092 2.741092 GGCGAACTCACCACCTCA 59.259 61.111 0.00 0.00 0.00 3.86
1798 2128 1.381872 CCTCCTCCGGTCCACATCT 60.382 63.158 0.00 0.00 0.00 2.90
1837 2167 2.848694 TGGGATGGAGAAATTGAGCTCT 59.151 45.455 16.19 0.00 0.00 4.09
1870 2200 0.464036 TCCTCCATGTCCCGAAATCG 59.536 55.000 0.00 0.00 39.44 3.34
1933 2263 2.507058 AGTATTGCTCTTCATGGCAGGA 59.493 45.455 0.00 0.00 39.68 3.86
1934 2264 2.928334 AGTATTGCTCTTCATGGCAGG 58.072 47.619 0.00 0.00 39.68 4.85
2017 2347 3.147629 CTCTCCTGAATGATTGGATGGC 58.852 50.000 0.00 0.00 0.00 4.40
2044 2374 2.757950 GCTGACAGGGGAGAGATCCATA 60.758 54.545 4.26 0.00 0.00 2.74
2137 2467 3.118775 CGATATCTTGTTGTGTCCTCCCA 60.119 47.826 0.34 0.00 0.00 4.37
2170 2500 1.741770 CCACGAAGGCTGCACTACC 60.742 63.158 0.50 0.00 0.00 3.18
2305 2635 5.319043 TCCATGAAACTTTTACCCTCTGT 57.681 39.130 0.00 0.00 0.00 3.41
2317 2647 4.713792 AGGAGTGTTCTTCCATGAAACT 57.286 40.909 0.00 0.00 0.00 2.66
2338 2668 9.330063 CAGAAGATTTTAACTATGCCATGAGTA 57.670 33.333 0.00 0.00 0.00 2.59
2368 2698 2.203070 GGCATCCGGGCTGTACTG 60.203 66.667 0.00 0.00 39.42 2.74
2563 2893 1.156736 CATGTTCTTCCGGCTCGTTT 58.843 50.000 0.00 0.00 0.00 3.60
2587 2917 3.161450 GGGCGCATGGAGACCCTA 61.161 66.667 10.83 0.00 39.42 3.53
2679 3013 1.701847 CAGTAGCCCCTTGGAGCATAT 59.298 52.381 0.00 0.00 0.00 1.78
2741 3079 0.879765 CTTGTTGCTGAAGAGGCCAG 59.120 55.000 5.01 0.00 34.88 4.85
2742 3080 1.174712 GCTTGTTGCTGAAGAGGCCA 61.175 55.000 5.01 0.00 38.95 5.36
2887 3235 8.821817 AGCAGTAACCCACCAAATATAAATTTT 58.178 29.630 0.00 0.00 32.87 1.82
2938 3286 9.436957 CAGACTGGTACTAACATAAGAATTGTT 57.563 33.333 0.00 0.00 40.30 2.83
2939 3287 8.594550 ACAGACTGGTACTAACATAAGAATTGT 58.405 33.333 7.51 0.00 0.00 2.71
2993 3344 9.160496 CTGAAGCACTGAATTAATCTCTTAACT 57.840 33.333 0.00 0.00 29.85 2.24
3001 3352 7.137426 CCATAAGCTGAAGCACTGAATTAATC 58.863 38.462 4.90 0.00 45.16 1.75
3090 3441 3.181503 GCTGCATCAACAACTCCTGTATG 60.182 47.826 0.00 0.00 37.23 2.39
3114 3465 4.336433 TGTTTTTCAGAGAGACCAAAGCAG 59.664 41.667 0.00 0.00 0.00 4.24
3115 3466 4.269183 TGTTTTTCAGAGAGACCAAAGCA 58.731 39.130 0.00 0.00 0.00 3.91
3116 3467 4.576463 TCTGTTTTTCAGAGAGACCAAAGC 59.424 41.667 0.00 0.00 46.77 3.51
3216 3571 5.010282 TGGAGGAGCCTTTTTATTTCTGTC 58.990 41.667 0.00 0.00 37.63 3.51
3256 3611 0.878416 TGCCAAATCGTGCTTACCAC 59.122 50.000 0.00 0.00 41.15 4.16
3259 3614 3.764885 AATCTGCCAAATCGTGCTTAC 57.235 42.857 0.00 0.00 0.00 2.34
3264 3619 1.067706 TGCCAAATCTGCCAAATCGTG 60.068 47.619 0.00 0.00 0.00 4.35
3266 3621 2.466846 GATGCCAAATCTGCCAAATCG 58.533 47.619 0.00 0.00 0.00 3.34
3267 3622 2.433239 AGGATGCCAAATCTGCCAAATC 59.567 45.455 0.00 0.00 0.00 2.17
3268 3623 2.169769 CAGGATGCCAAATCTGCCAAAT 59.830 45.455 0.00 0.00 0.00 2.32
3269 3624 1.551430 CAGGATGCCAAATCTGCCAAA 59.449 47.619 0.00 0.00 0.00 3.28
3270 3625 1.187974 CAGGATGCCAAATCTGCCAA 58.812 50.000 0.00 0.00 0.00 4.52
3273 3628 1.407979 CTTCCAGGATGCCAAATCTGC 59.592 52.381 0.00 0.00 31.97 4.26
3359 3714 8.585018 CAGTTATTAAACCCAGAAAAGATTGGT 58.415 33.333 0.00 0.00 36.15 3.67
3432 3787 9.584008 CCAGGTCTATTGGAGTAGTATAAGTAA 57.416 37.037 0.00 0.00 37.96 2.24
3433 3788 8.168725 CCCAGGTCTATTGGAGTAGTATAAGTA 58.831 40.741 0.00 0.00 37.96 2.24
3434 3789 7.011382 CCCAGGTCTATTGGAGTAGTATAAGT 58.989 42.308 0.00 0.00 37.96 2.24
3435 3790 7.011382 ACCCAGGTCTATTGGAGTAGTATAAG 58.989 42.308 0.00 0.00 37.96 1.73
3436 3791 6.930475 ACCCAGGTCTATTGGAGTAGTATAA 58.070 40.000 0.00 0.00 37.96 0.98
3437 3792 6.541264 ACCCAGGTCTATTGGAGTAGTATA 57.459 41.667 0.00 0.00 37.96 1.47
3438 3793 5.395611 GACCCAGGTCTATTGGAGTAGTAT 58.604 45.833 9.67 0.00 41.57 2.12
3439 3794 4.801164 GACCCAGGTCTATTGGAGTAGTA 58.199 47.826 9.67 0.00 41.57 1.82
3440 3795 3.644335 GACCCAGGTCTATTGGAGTAGT 58.356 50.000 9.67 0.00 41.57 2.73
3452 3807 1.550976 CCACAGTAGAAGACCCAGGTC 59.449 57.143 8.88 8.88 44.86 3.85
3453 3808 1.149288 TCCACAGTAGAAGACCCAGGT 59.851 52.381 0.00 0.00 0.00 4.00
3454 3809 1.938585 TCCACAGTAGAAGACCCAGG 58.061 55.000 0.00 0.00 0.00 4.45
3496 3867 9.258826 CACTCATTTCTTGTTCTCCAGATATAG 57.741 37.037 0.00 0.00 0.00 1.31
3507 3878 7.433425 CCTTGAAACTTCACTCATTTCTTGTTC 59.567 37.037 0.00 0.00 36.83 3.18
3555 3926 5.811100 GCAGTTGTTAGGTGTAAGATAGACC 59.189 44.000 0.00 0.00 42.12 3.85
3556 3927 6.531948 CAGCAGTTGTTAGGTGTAAGATAGAC 59.468 42.308 0.00 0.00 0.00 2.59
3557 3928 6.631016 CAGCAGTTGTTAGGTGTAAGATAGA 58.369 40.000 0.00 0.00 0.00 1.98
3558 3929 5.292101 GCAGCAGTTGTTAGGTGTAAGATAG 59.708 44.000 0.00 0.00 35.77 2.08
3589 3960 1.153549 CCTAGAGCGGAACAGGCAC 60.154 63.158 0.00 0.00 0.00 5.01
3603 3974 2.547642 GGCTGCAGCTATCTGAACCTAG 60.548 54.545 35.82 0.00 42.95 3.02
3631 4002 3.087253 TCGGGGTATGTGCTGGGG 61.087 66.667 0.00 0.00 0.00 4.96
3632 4003 1.046472 TACTCGGGGTATGTGCTGGG 61.046 60.000 0.00 0.00 0.00 4.45
3633 4004 1.048601 ATACTCGGGGTATGTGCTGG 58.951 55.000 0.00 0.00 39.43 4.85
3640 4011 0.399376 TGGTGCCATACTCGGGGTAT 60.399 55.000 0.00 0.00 41.38 2.73
3641 4012 1.001888 TGGTGCCATACTCGGGGTA 59.998 57.895 0.00 0.00 34.62 3.69
3642 4013 2.285069 TGGTGCCATACTCGGGGT 60.285 61.111 0.00 0.00 0.00 4.95
3643 4014 2.505982 CTGGTGCCATACTCGGGG 59.494 66.667 0.00 0.00 0.00 5.73
3644 4015 2.063979 TCCTGGTGCCATACTCGGG 61.064 63.158 0.00 0.00 0.00 5.14
3645 4016 1.144057 GTCCTGGTGCCATACTCGG 59.856 63.158 0.00 0.00 0.00 4.63
3646 4017 0.460284 GTGTCCTGGTGCCATACTCG 60.460 60.000 0.00 0.00 0.00 4.18
3653 4024 1.302033 CTGTCTGTGTCCTGGTGCC 60.302 63.158 0.00 0.00 0.00 5.01
3655 4026 0.319728 CTCCTGTCTGTGTCCTGGTG 59.680 60.000 0.00 0.00 0.00 4.17
3697 4433 3.242870 GCAGATTGTAGCGAATTCTTGGG 60.243 47.826 3.52 0.00 0.00 4.12
3707 4443 1.324736 GTTCCGAAGCAGATTGTAGCG 59.675 52.381 0.00 0.00 35.48 4.26
3724 4460 0.107945 CAGGAGGTGCAGCTAGGTTC 60.108 60.000 20.22 5.94 0.00 3.62
3730 4466 3.325753 GGTCCAGGAGGTGCAGCT 61.326 66.667 20.31 20.31 35.89 4.24
3731 4467 3.325753 AGGTCCAGGAGGTGCAGC 61.326 66.667 8.11 8.11 35.89 5.25
3732 4468 2.667418 CAGGTCCAGGAGGTGCAG 59.333 66.667 0.00 0.00 35.89 4.41
3733 4469 3.640407 GCAGGTCCAGGAGGTGCA 61.640 66.667 15.62 0.00 35.21 4.57
3734 4470 3.322318 GAGCAGGTCCAGGAGGTGC 62.322 68.421 13.37 13.37 35.31 5.01
3736 4472 2.522198 ATCGAGCAGGTCCAGGAGGT 62.522 60.000 0.00 0.00 35.89 3.85
3737 4473 0.468214 TATCGAGCAGGTCCAGGAGG 60.468 60.000 0.00 0.00 0.00 4.30
3738 4474 1.403814 TTATCGAGCAGGTCCAGGAG 58.596 55.000 0.00 0.00 0.00 3.69
3739 4475 1.688735 CATTATCGAGCAGGTCCAGGA 59.311 52.381 0.00 0.00 0.00 3.86
3740 4476 1.270518 CCATTATCGAGCAGGTCCAGG 60.271 57.143 0.00 0.00 0.00 4.45
3759 4495 2.681152 ATTTCGTTTCGTGTGCTTCC 57.319 45.000 0.00 0.00 0.00 3.46
3761 4497 2.116366 GCAATTTCGTTTCGTGTGCTT 58.884 42.857 0.00 0.00 0.00 3.91
3762 4498 1.333619 AGCAATTTCGTTTCGTGTGCT 59.666 42.857 0.00 0.00 0.00 4.40
3763 4499 1.753956 AGCAATTTCGTTTCGTGTGC 58.246 45.000 0.00 0.00 0.00 4.57
3764 4500 3.867665 TGTAGCAATTTCGTTTCGTGTG 58.132 40.909 0.00 0.00 0.00 3.82
3765 4501 4.742438 ATGTAGCAATTTCGTTTCGTGT 57.258 36.364 0.00 0.00 0.00 4.49
3772 4508 4.002982 TCAGCAGAATGTAGCAATTTCGT 58.997 39.130 0.00 0.00 39.31 3.85
3827 4563 1.611474 AATCTGAGCAGCGCAGAGGA 61.611 55.000 29.38 11.45 42.83 3.71
3828 4564 1.152989 GAATCTGAGCAGCGCAGAGG 61.153 60.000 29.38 6.28 42.83 3.69
3838 4574 1.129437 GTTGTGGCTTCGAATCTGAGC 59.871 52.381 0.00 0.00 0.00 4.26
3841 4577 2.160417 GGAAGTTGTGGCTTCGAATCTG 59.840 50.000 0.00 0.00 44.17 2.90
3845 4581 1.134220 ACAGGAAGTTGTGGCTTCGAA 60.134 47.619 0.00 0.00 44.17 3.71
3848 4584 2.952310 AGAAACAGGAAGTTGTGGCTTC 59.048 45.455 0.00 0.00 41.19 3.86
3860 4596 1.000955 GAAGGTGCTCGAGAAACAGGA 59.999 52.381 18.75 0.00 0.00 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.